Are we allowed to deviate off the South Downs way at any point?

Generally, as long as you are on rights of way and not crossing fences or ploughed fields you will be OK, though I don't think there's many places where coming off the SDW actually gains any time.

One section is after the base at Washington. There are two alternative routes back onto the South Downs, via the road off 122126 or the path passing Tilley's Farm - can these be used?

At Washington, I think the path you're referring to is actually signposted as a SDW alternative route. It is perfectly acceptable and I'm sure most teams use it.

At the Devil's Dyke base, do we have to stay on the South Downs until we meet the road and move walk up the road or can we take the footpath which takes us almost directly to the base?

At the Dyke, you should deviate off the SDW and head straight for the stile opposite the pub and thus into the checkpoint. There is no need to walk up the road.

We have a scout team that doesn't quite make the "minimum 48 years" - is there any flexibility?

We always advise teams in this position to enter the Open class one last time, as they will qualify the following year for class S. The age limit was brought in because County were uncomfortable with the possibility of groups of under 12s being out without a leader! This rule ensures that at least one of the team walking at any time will be 12 or over.